Revision: 20965
http://sourceforge.net/p/jmol/code/20965
Author: hansonr
Date: 2016-02-27 18:59:52 +0000 (Sat, 27 Feb 2016)
Log Message:
-----------
Jmol.___JmolVersion="14.4.3_2016.02.27"
bug fix: [function:"yyy",Function:"zzz"] fails to retain key capitalization
after first entry for special names
bug fix: (JavaScript only) polyhedra not saved in state
bug fix: (Applet) broken image in coverImage
bug fix: polyhedra DELETE can crash Jmol if polyhedra are not colored
Modified Paths:
--------------
branches/v14_4/Jmol/src/org/jmol/script/SV.java
branches/v14_4/Jmol/src/org/jmol/script/ScriptCompiler.java
branches/v14_4/Jmol/src/org/jmol/script/T.java
branches/v14_4/Jmol/src/org/jmol/shapespecial/Polyhedra.java
branches/v14_4/Jmol/src/org/jmol/shapespecial/Polyhedron.java
branches/v14_4/Jmol/src/org/jmol/util/MeshSlicer.java
branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/script/SV.java
trunk/Jmol/src/org/jmol/script/ScriptCompiler.java
trunk/Jmol/src/org/jmol/script/T.java
trunk/Jmol/src/org/jmol/shapespecial/Polyhedra.java
trunk/Jmol/src/org/jmol/shapespecial/Polyhedron.java
trunk/Jmol/src/org/jmol/util/MeshSlicer.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: branches/v14_4/Jmol/src/org/jmol/script/SV.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/script/SV.java 2016-02-18 04:47:00 UTC
(rev 20964)
+++ branches/v14_4/Jmol/src/org/jmol/script/SV.java 2016-02-27 18:59:52 UTC
(rev 20965)
@@ -287,6 +287,8 @@
return getVariableAD((double[]) x);
if (AU.isAS(x))
return getVariableAS((String[]) x);
+ //NOTE: isAP(x) does not return TRUE for Atom[] in JavaScript
+ // only occurrence of this was for Polyhedron.getInfo()
if (AU.isAP(x))
return getVariableAP((T3[]) x);
if (AU.isAII(x))
Modified: branches/v14_4/Jmol/src/org/jmol/script/ScriptCompiler.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/script/ScriptCompiler.java 2016-02-18
04:47:00 UTC (rev 20964)
+++ branches/v14_4/Jmol/src/org/jmol/script/ScriptCompiler.java 2016-02-27
18:59:52 UTC (rev 20965)
@@ -1010,7 +1010,8 @@
private int getPrefixToken() {
ident = script.substring(ichToken, ichToken + cchToken);
identLC = ident.toLowerCase();
- boolean isUserVar = lastToken.tok != T.per && !isDotDot &&
isContextVariable(identLC);
+ boolean isUserVar = lastToken.tok != T.per && !isDotDot
+ && isContextVariable(identLC);
String myName = ident;//(isUserVar ? ident : null);
String preserveCase = null;
if (nTokens == 0)
@@ -1048,14 +1049,21 @@
theToken = T.tv(theToken.tok, theToken.intValue, ident);
} else {
theToken = T.getTokenFromName(identLC);
- if (theToken != null
- && (lastToken.tok == T.per || lastToken.tok == T.leftsquare))
- theToken = T.o(theToken.tok, ident);
+ if (theToken != null)
+ switch (lastToken.tok) {
+ case T.per:
+ case T.leftsquare:
+ case T.comma:
+ // looking out for hash names
+ theToken = T.o(theToken.tok, ident);
+ }
}
if (theToken == null) {
// myName is just in case this is being used as a key to a hash
- theToken = SV.newSV((identLC.indexOf("property_") == 0 ? T.property :
T.identifier), Integer.MAX_VALUE, ident).setName(myName);
+ theToken = SV.newSV(
+ (identLC.indexOf("property_") == 0 ? T.property : T.identifier),
+ Integer.MAX_VALUE, ident).setName(myName);
}
return theTok = theToken.tok;
}
Modified: branches/v14_4/Jmol/src/org/jmol/script/T.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/script/T.java 2016-02-18 04:47:00 UTC
(rev 20964)
+++ branches/v14_4/Jmol/src/org/jmol/script/T.java 2016-02-27 18:59:52 UTC
(rev 20965)
@@ -1414,8 +1414,6 @@
public static T getTokenFromName(String name) {
// this one needs to NOT be lower case for ScriptCompiler
- if (name == null)
- System.out.println("???");
return tokenMap.get(name);
}
Modified: branches/v14_4/Jmol/src/org/jmol/shapespecial/Polyhedra.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/shapespecial/Polyhedra.java
2016-02-18 04:47:00 UTC (rev 20964)
+++ branches/v14_4/Jmol/src/org/jmol/shapespecial/Polyhedra.java
2016-02-27 18:59:52 UTC (rev 20965)
@@ -355,8 +355,9 @@
for (int i = polyhedronCount; --i >= 0;) {
Polyhedron p = polyhedrons[i];
p.info = null;
- int mi = (p.id == null ? p.centralAtom.mi : p.modelIndex);
- if (mi == modelIndex) {
+ if (p.modelIndex > modelIndex) {
+ p.modelIndex--;
+ } else if (p.modelIndex == modelIndex) {
polyhedronCount--;
polyhedrons = (Polyhedron[]) AU.deleteElements(polyhedrons, i, 1);
}
@@ -453,7 +454,7 @@
if (property == "allInfo") {
Lst<Map<String, Object>> info = new Lst<Map<String, Object>>();
for (int i = polyhedronCount; --i >= 0;)
- info.addLast(polyhedrons[i].getInfo(vwr, true));
+ info.addLast(polyhedrons[i].getInfo(vwr, false));
data[1] = info;
return true;
}
@@ -461,7 +462,7 @@
p = findPoly(id, iatom, true);
if (p == null)
return false;
- data[1] = p.getInfo(vwr, true);
+ data[1] = p.getInfo(vwr, false);
return true;
}
return getPropShape(property, data);
@@ -504,7 +505,7 @@
public Lst<Map<String, Object>> getShapeDetail() {
Lst<Map<String, Object>> lst = new Lst<Map<String, Object>>();
for (int i = 0; i < polyhedronCount; i++)
- lst.addLast(polyhedrons[i].getInfo(vwr, true));
+ lst.addLast(polyhedrons[i].getInfo(vwr, false));
return lst;
}
@@ -526,7 +527,7 @@
for (int i = 0; i < polyhedronCount; ++i) {
Polyhedron p = polyhedrons[i];
if (bs.get(i)) {
- if (p.id == null)
+ if (colixes != null && p.id == null)
setColixAndPalette(C.INHERIT_ALL, pid, p.centralAtom.i);
continue;
}
@@ -1078,7 +1079,7 @@
if (p.id == null) {
if (ms.at[p.centralAtom.i].isDeleted())
p.isValid = false;
- p.visibilityFlags = (p.visible && bsModels.get(p.centralAtom.mi)
+ p.visibilityFlags = (p.visible && bsModels.get(p.modelIndex)
&& !ms.isAtomHidden(p.centralAtom.i)
&& !ms.at[p.centralAtom.i].isDeleted() ? vf : 0);
if (p.visibilityFlags != 0)
Modified: branches/v14_4/Jmol/src/org/jmol/shapespecial/Polyhedron.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/shapespecial/Polyhedron.java
2016-02-18 04:47:00 UTC (rev 20964)
+++ branches/v14_4/Jmol/src/org/jmol/shapespecial/Polyhedron.java
2016-02-27 18:59:52 UTC (rev 20965)
@@ -77,10 +77,14 @@
int[][] triangles, int triangleCount, int[][] faces, V3[] normals, BS
bsFlat, boolean collapsed, float distanceRef) {
this.distanceRef = distanceRef;
- centralAtom = (id == null ? (Atom) atomOrPt : null);
- center = (centralAtom == null ? (P3) atomOrPt : null);
- this.modelIndex = (centralAtom == null ? modelIndex : centralAtom.mi);
- this.id = id;
+ if (id == null) {
+ centralAtom = (Atom) atomOrPt;
+ this.modelIndex = centralAtom.mi;
+ } else {
+ this.id = id;
+ center = atomOrPt;
+ this.modelIndex = modelIndex;
+ }
this.nVertices = vertexCount;
this.vertices = new P3[nPoints + 1];
this.normals = new V3[triangleCount];
@@ -177,12 +181,43 @@
return ai;
}
- Map<String, Object> getInfo(Viewer vwr, boolean isAll) {
- if (isAll && this.info != null && !Logger.debugging)
+ Map<String, Object> getInfo(Viewer vwr, boolean isState) {
+ if (!isState && this.info != null && !Logger.debugging)
return this.info;
Map<String, Object> info = new Hashtable<String, Object>();
- int mi = (id == null ? centralAtom.mi : modelIndex);
- if (isAll) {
+
+ info.put("vertexCount", Integer.valueOf(nVertices));
+
+ // get COPY of vertices to prevent script variable from referencing Atom
+ int nv = (isState ? vertices.length : nVertices);
+ P3[] pts = new P3[nv];
+ for (int i = 0; i < nv; i++)
+ pts[i] = P3.newP(vertices[i]);
+ info.put("vertices", pts);
+
+ int[] elemNos = new int[nVertices];
+ for (int i = 0; i < nVertices; i++) {
+ P3 pt = vertices[i];
+ elemNos[i] = (pt instanceof Node ? ((Node) pt).getElementNumber()
+ : pt instanceof Point3fi ? ((Point3fi) pt).sD : -2);
+ }
+ info.put("elemNos", elemNos);
+
+ if (id == null) {
+ info.put("atomIndex", Integer.valueOf(centralAtom.i));
+ } else {
+ info.put("id", id);
+ info.put("center", P3.newP(center));
+ info.put("color", C.getHexCode(colix));
+ info.put("colorEdge", C.getHexCode(colixEdge == 0 ? colix : colixEdge));
+ if (offset != null)
+ info.put("offset", offset);
+ if (scale != 1)
+ info.put("scale", Float.valueOf(scale));
+ }
+ if (id != null || !isState)
+ info.put("modelIndex", Integer.valueOf(modelIndex));
+ if (!isState) {
this.info = info;
if (id == null) {
info.put("center", P3.newP(centralAtom));
@@ -196,40 +231,38 @@
}
info.put("triangleCount", Integer.valueOf(triangles.length));
info.put("volume", getVolume());
+
String[] names = new String[nVertices];
+ int[] indices = new int[nVertices];
for (int i = nVertices; --i >= 0;) {
P3 pt = vertices[i];
- names[i] = (pt instanceof Node ? ((Node) pt).getAtomName()
+ boolean isNode = pt instanceof Node;
+ names[i] = (isNode ? ((Node) pt).getAtomName()
: pt instanceof Point3fi ? Elements
.elementSymbolFromNumber(((Point3fi) pt).sD) : "");
+ indices[i] = (isNode ? ((Node) pt).getIndex() : -1);
}
+ info.put("atomNames", names);
+ info.put("vertexIndices", indices);
+
if (faces != null)
info.put("faceCount", Integer.valueOf(faces.length));
- info.put("atomNames", names);
+
if (smarts != null)
info.put("smarts", smarts);
if (smiles != null)
info.put("smiles", smiles);
if (polySmiles != null)
info.put("polySmiles", polySmiles);
+
if (pointGroup != null)
info.put("pointGroup", pointGroup.getPointGroupName());
if (pointGroupFamily != null)
info.put("pointGroupFamily", pointGroupFamily.getPointGroupName());
}
- if (id != null) {
- info.put("id", id);
- info.put("modelIndex", Integer.valueOf(mi));
- info.put("color", C.getHexCode(colix));
- info.put("colorEdge", C.getHexCode(colixEdge == 0 ? colix : colixEdge));
- if (offset != null)
- info.put("offset", offset);
- if (scale != 1)
- info.put("scale", Float.valueOf(scale));
- }
if (faces != null)
info.put("faces", faces);
- if (!isAll || Logger.debugging) {
+ if (isState || Logger.debugging) {
info.put("bsFlat", bsFlat);
if (collapsed)
info.put("collapsed", Boolean.valueOf(collapsed));
@@ -241,22 +274,6 @@
info.put("normals", n);
info.put("triangles", AU.arrayCopyII(triangles, triangles.length));
}
- info.put("vertexCount", Integer.valueOf(nVertices));
- if (center == null) {
- info.put("atomIndex", Integer.valueOf(centralAtom.i));
- } else {
- info.put("id", id);
- info.put("center", P3.newP(center));
- }
- info.put("vertices",
- AU.arrayCopyPt(vertices, (isAll ? nVertices : vertices.length)));
- int[] elemNos = new int[nVertices];
- for (int i = 0; i < nVertices; i++) {
- P3 pt = vertices[i];
- elemNos[i] = (pt instanceof Node ? ((Node) pt).getElementNumber()
- : pt instanceof Point3fi ? ((Point3fi) pt).sD : -2);
- }
- info.put("elemNos", elemNos);
return info;
}
@@ -330,7 +347,7 @@
String getState(Viewer vwr) {
String ident = (id == null ? "({"+centralAtom.i+"})" : "ID " +
Escape.e(id));
- return " polyhedron" + " @{" + Escape.e(getInfo(vwr, false)) + "} "
+ return " polyhedron" + " @{" + Escape.e(getInfo(vwr, true)) + "} "
+ (isFullyLit ? " fullyLit" : "") + ";"
+ (visible ? "" : "polyhedra " + ident + " off;") + "\n";
}
Modified: branches/v14_4/Jmol/src/org/jmol/util/MeshSlicer.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/util/MeshSlicer.java 2016-02-18
04:47:00 UTC (rev 20964)
+++ branches/v14_4/Jmol/src/org/jmol/util/MeshSlicer.java 2016-02-27
18:59:52 UTC (rev 20965)
@@ -241,7 +241,7 @@
wPlane = 0;
}
}
-
+
if (fData == null) {
if (tokType == T.decimal && bsSource != null) {
if (m.vertexSource == null)
@@ -257,8 +257,7 @@
if (m.pc == 0) {
for (int i = m.mergeVertexCount0; i < m.vc; i++) {
if (Float.isNaN(fData[i])
- || checkSlab(tokType, m.vs[i], fData[i], distance,
- bsSource) > 0)
+ || checkSlab(tokType, m.vs[i], fData[i], distance, bsSource) > 0)
m.bsSlabDisplay.clear(i);
}
return;
@@ -266,40 +265,58 @@
if (ptCenters != null || isGhost)
andCap = false; // can only cap faces, and no capping of ghosts
if (andCap && capper == null)
- capper = ((MeshCapper)
Interface.getInterface("org.jmol.util.MeshCapper", m.vwr, "script")).set(this);
+ capper = ((MeshCapper) Interface.getInterface("org.jmol.util.MeshCapper",
+ m.vwr, "script")).set(this);
if (capper != null)
capper.clear();
double absD = Math.abs(distance);
Map<String, Integer> mapEdge = new Hashtable<String, Integer>();
+ BS bsD = BS.newN(m.vc);
+ float[] d = new float[m.vc];
+ float d1 = 0, d2 = 0, d3 = 0, valA, valB, valC;
for (int i = m.mergePolygonCount0, iLast = m.pc; i < iLast; i++) {
- float d1, d2, d3, valA, valB, valC;
- int[] face = m.setABC(i);
+ int[] face = m.setABC(i);
if (face == null)
continue;
BS bsSlab = (m.bsSlabGhost != null && m.bsSlabGhost.get(i) ?
m.bsSlabGhost
: m.bsSlabDisplay);
int check1 = face[MeshSurface.P_CHECK];
int iContour = (m.dataOnly ? 0 : face[MeshSurface.P_CONTOUR]);
- T3 vA = m.vs[m.iA];
- T3 vB = m.vs[m.iB];
- T3 vC = m.vs[m.iC];
- valA = fData[m.iA];
- valB = fData[m.iB];
- valC = fData[m.iC];
+ int ia = m.iA;
+ int ib = m.iB;
+ int ic = m.iC;
+ T3 vA = m.vs[ia];
+ T3 vB = m.vs[ib];
+ T3 vC = m.vs[ic];
+ valA = fData[ia];
+ valB = fData[ib];
+ valC = fData[ic];
if (m.vertexSource != null) {
- sources[0] = m.vertexSource[m.iA];
- sources[1] = m.vertexSource[m.iB];
- sources[2] = m.vertexSource[m.iC];
+ sources[0] = m.vertexSource[ia];
+ sources[1] = m.vertexSource[ib];
+ sources[2] = m.vertexSource[ic];
}
- int thisSet = (m.vertexSets == null ? 0 : m.vertexSets[m.iA]);
- d1 = checkSlab(tokType, vA, valA, (bsSource == null ? distance
- : sources[0]), bsSource);
- d2 = checkSlab(tokType, vB, valB, (bsSource == null ? distance
- : sources[1]), bsSource);
- d3 = checkSlab(tokType, vC, valC, (bsSource == null ? distance
- : sources[2]), bsSource);
+ if (!bsD.get(ia)) {
+ bsD.set(ia);
+ d[ia] = checkSlab(tokType, vA, valA, (bsSource == null ? distance
+ : sources[0]), bsSource);
+ }
+ if (!bsD.get(ib)) {
+ bsD.set(ib);
+ d[ib] = checkSlab(tokType, vB, valB, (bsSource == null ? distance
+ : sources[1]), bsSource);
+ }
+ if (!bsD.get(ic)) {
+ bsD.set(ic);
+ d[ic] = checkSlab(tokType, vC, valC, (bsSource == null ? distance
+ : sources[2]), bsSource);
+ }
+ d1 = d[ia];
+ d2 = d[ib];
+ d3 = d[ic];
int test1 = (d1 != 0 && d1 < 0 ? 1 : 0) + (d2 != 0 && d2 < 0 ? 2 : 0)
+ (d3 != 0 && d3 < 0 ? 4 : 0);
+ int thisSet = (m.vertexSets == null ? 0 : m.vertexSets[ia]);
/*
if (iA == 955 || iB == 955 || iC == 955) {
@@ -340,8 +357,7 @@
case 6:
// BC on same side
if (ptCenters == null)
- p = new P3[] {
- interpolatePoint(vA, vB, -d1, d2, valA, valB, 0),
+ p = new P3[] { interpolatePoint(vA, vB, -d1, d2, valA, valB, 0),
interpolatePoint(vA, vC, -d1, d3, valA, valC, 1) };
else
p = new P3[] {
@@ -352,8 +368,7 @@
case 5:
//AC on same side
if (ptCenters == null)
- p = new P3[] {
- interpolatePoint(vB, vA, -d2, d1, valB, valA, 1),
+ p = new P3[] { interpolatePoint(vB, vA, -d2, d1, valB, valA, 1),
interpolatePoint(vB, vC, -d2, d3, valB, valC, 0) };
else
p = new P3[] {
@@ -364,8 +379,7 @@
case 4:
//AB on same side need A-C, B-C
if (ptCenters == null)
- p = new P3[] {
- interpolatePoint(vC, vA, -d3, d1, valC, valA, 0),
+ p = new P3[] { interpolatePoint(vC, vA, -d3, d1, valC, valA, 0),
interpolatePoint(vC, vB, -d3, d2, valC, valB, 1) };
else
p = new P3[] {
@@ -405,32 +419,32 @@
boolean tossBC = (test1 == 1);
if (tossBC || isGhost) {
// 1: BC on side to toss -- +tossBC+isGhost -tossBC+isGhost
- if (!getDE(fracs, 0, m.iA, m.iB, m.iC, tossBC))
+ if (!getDE(fracs, 0, ia, ib, ic, tossBC))
break;
if (iD < 0)
- iD = addIntersectionVertex(p[0], values[0], sources[0],
- thisSet, mapEdge, m.iA, m.iB);
+ iD = addIntersectionVertex(p[0], values[0], sources[0], thisSet,
+ mapEdge, ia, ib);
if (iE < 0)
- iE = addIntersectionVertex(p[1], values[1], sources[0],
- thisSet, mapEdge, m.iA, m.iC);
+ iE = addIntersectionVertex(p[1], values[1], sources[0], thisSet,
+ mapEdge, ia, ic);
bs = (tossBC ? bsSlab : m.bsSlabGhost);
- m.addPolygonV3(m.iA, iD, iE, check1 & 5 | 2, iContour, 0, bs);
+ m.addPolygonV3(ia, iD, iE, check1 & 5 | 2, iContour, 0, bs);
if (!isGhost)
break;
}
// BC on side to keep -- -tossBC+isGhost, +tossBC+isGhost
- if (!getDE(fracs, 1, m.iA, m.iC, m.iB, tossBC))
+ if (!getDE(fracs, 1, ia, ic, ib, tossBC))
break;
bs = (tossBC ? m.bsSlabGhost : bsSlab);
if (iE < 0) {
iE = addIntersectionVertex(p[0], values[0], sources[1], thisSet,
- mapEdge, m.iA, m.iB);
- m.addPolygonV3(iE, m.iB, m.iC, check1 & 3, iContour, 0, bs);
+ mapEdge, ia, ib);
+ m.addPolygonV3(iE, ib, ic, check1 & 3, iContour, 0, bs);
}
if (iD < 0) {
iD = addIntersectionVertex(p[1], values[1], sources[2], thisSet,
- mapEdge, m.iA, m.iC);
- m.addPolygonV3(iD, iE, m.iC, check1 & 4 | 1, iContour, 0, bs);
+ mapEdge, ia, ic);
+ m.addPolygonV3(iD, iE, ic, check1 & 4 | 1, iContour, 0, bs);
}
break;
case 5:
@@ -444,32 +458,32 @@
boolean tossAC = (test1 == 2);
if (tossAC || isGhost) {
//AC on side to toss
- if (!getDE(fracs, 0, m.iB, m.iC, m.iA, tossAC))
+ if (!getDE(fracs, 0, ib, ic, ia, tossAC))
break;
bs = (tossAC ? bsSlab : m.bsSlabGhost);
if (iE < 0)
- iE = addIntersectionVertex(p[0], values[0], sources[1],
- thisSet, mapEdge, m.iB, m.iA);
+ iE = addIntersectionVertex(p[0], values[0], sources[1], thisSet,
+ mapEdge, ib, ia);
if (iD < 0)
- iD = addIntersectionVertex(p[1], values[1], sources[1],
- thisSet, mapEdge, m.iB, m.iC);
- m.addPolygonV3(iE, m.iB, iD, check1 & 3 | 4, iContour, 0, bs);
+ iD = addIntersectionVertex(p[1], values[1], sources[1], thisSet,
+ mapEdge, ib, ic);
+ m.addPolygonV3(iE, ib, iD, check1 & 3 | 4, iContour, 0, bs);
if (!isGhost)
break;
}
// AC on side to keep
- if (!getDE(fracs, 1, m.iB, m.iA, m.iC, tossAC))
+ if (!getDE(fracs, 1, ib, ia, ic, tossAC))
break;
bs = (tossAC ? m.bsSlabGhost : bsSlab);
if (iD < 0) {
iD = addIntersectionVertex(p[0], values[0], sources[0], thisSet,
- mapEdge, m.iB, m.iA);
- m.addPolygonV3(m.iA, iD, m.iC, check1 & 5, iContour, 0, bs);
+ mapEdge, ib, ia);
+ m.addPolygonV3(ia, iD, ic, check1 & 5, iContour, 0, bs);
}
if (iE < 0) {
iE = addIntersectionVertex(p[1], values[1], sources[2], thisSet,
- mapEdge, m.iB, m.iC);
- m.addPolygonV3(iD, iE, m.iC, check1 & 2 | 1, iContour, 0, bs);
+ mapEdge, ib, ic);
+ m.addPolygonV3(iD, iE, ic, check1 & 2 | 1, iContour, 0, bs);
}
break;
case 4:
@@ -482,32 +496,32 @@
//
boolean tossAB = (test1 == 4);
if (tossAB || isGhost) {
- if (!getDE(fracs, 0, m.iC, m.iA, m.iB, tossAB))
+ if (!getDE(fracs, 0, ic, ia, ib, tossAB))
break;
if (iD < 0)
- iD = addIntersectionVertex(p[0], values[0], sources[2],
- thisSet, mapEdge, m.iA, m.iC); //CA
+ iD = addIntersectionVertex(p[0], values[0], sources[2], thisSet,
+ mapEdge, ia, ic); //CA
if (iE < 0)
- iE = addIntersectionVertex(p[1], values[1], sources[2],
- thisSet, mapEdge, m.iB, m.iC); //CB
+ iE = addIntersectionVertex(p[1], values[1], sources[2], thisSet,
+ mapEdge, ib, ic); //CB
bs = (tossAB ? bsSlab : m.bsSlabGhost);
- m.addPolygonV3(iD, iE, m.iC, check1 & 6 | 1, iContour, 0, bs);
+ m.addPolygonV3(iD, iE, ic, check1 & 6 | 1, iContour, 0, bs);
if (!isGhost)
break;
}
//AB on side to keep
- if (!getDE(fracs, 1, m.iC, m.iB, m.iA, tossAB))
+ if (!getDE(fracs, 1, ic, ib, ia, tossAB))
break;
bs = (tossAB ? m.bsSlabGhost : bsSlab);
if (iE < 0) {
iE = addIntersectionVertex(p[0], values[0], sources[0], thisSet,
- mapEdge, m.iA, m.iC); //CA
- m.addPolygonV3(m.iA, m.iB, iE, check1 & 5, iContour, 0, bs);
+ mapEdge, ia, ic); //CA
+ m.addPolygonV3(ia, ib, iE, check1 & 5, iContour, 0, bs);
}
if (iD < 0) {
iD = addIntersectionVertex(p[1], values[1], sources[1], thisSet,
- mapEdge, m.iB, m.iC); //CB
- m.addPolygonV3(iE, m.iB, iD, check1 & 2 | 4, iContour, 0, bs);
+ mapEdge, ib, ic); //CB
+ m.addPolygonV3(iE, ib, iD, check1 & 2 | 4, iContour, 0, bs);
}
break;
}
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2016-02-18
04:47:00 UTC (rev 20964)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2016-02-27
18:59:52 UTC (rev 20965)
@@ -7,8 +7,17 @@
# see also http://chemapps.stolaf.edu/jmol/zip for daily updates
-Jmol.___JmolVersion="14.4.3_2016.02.17"
+Jmol.___JmolVersion="14.4.3_2016.02.27"
+
+bug fix: [function:"yyy",Function:"zzz"] fails to retain key capitalization
after first entry for special names
+bug fix: (JavaScript only) polyhedra not saved in state
+bug fix: (Applet) broken image in coverImage
+bug fix: polyhedra DELETE can crash Jmol if polyhedra are not colored
+
+
+JmolVersion="14.4.3_2016.02.18"
+
bug fix: slab/depth SET do not behave properly
bug fix: select VISIBLE is not properly set based on slab/depth SET
Modified: trunk/Jmol/src/org/jmol/script/SV.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/SV.java 2016-02-18 04:47:00 UTC (rev
20964)
+++ trunk/Jmol/src/org/jmol/script/SV.java 2016-02-27 18:59:52 UTC (rev
20965)
@@ -287,6 +287,8 @@
return getVariableAD((double[]) x);
if (AU.isAS(x))
return getVariableAS((String[]) x);
+ //NOTE: isAP(x) does not return TRUE for Atom[] in JavaScript
+ // only occurrence of this was for Polyhedron.getInfo()
if (AU.isAP(x))
return getVariableAP((T3[]) x);
if (AU.isAII(x))
Modified: trunk/Jmol/src/org/jmol/script/ScriptCompiler.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptCompiler.java 2016-02-18 04:47:00 UTC
(rev 20964)
+++ trunk/Jmol/src/org/jmol/script/ScriptCompiler.java 2016-02-27 18:59:52 UTC
(rev 20965)
@@ -1010,7 +1010,8 @@
private int getPrefixToken() {
ident = script.substring(ichToken, ichToken + cchToken);
identLC = ident.toLowerCase();
- boolean isUserVar = lastToken.tok != T.per && !isDotDot &&
isContextVariable(identLC);
+ boolean isUserVar = lastToken.tok != T.per && !isDotDot
+ && isContextVariable(identLC);
String myName = ident;//(isUserVar ? ident : null);
String preserveCase = null;
if (nTokens == 0)
@@ -1048,14 +1049,21 @@
theToken = T.tv(theToken.tok, theToken.intValue, ident);
} else {
theToken = T.getTokenFromName(identLC);
- if (theToken != null
- && (lastToken.tok == T.per || lastToken.tok == T.leftsquare))
- theToken = T.o(theToken.tok, ident);
+ if (theToken != null)
+ switch (lastToken.tok) {
+ case T.per:
+ case T.leftsquare:
+ case T.comma:
+ // looking out for hash names
+ theToken = T.o(theToken.tok, ident);
+ }
}
if (theToken == null) {
// myName is just in case this is being used as a key to a hash
- theToken = SV.newSV((identLC.indexOf("property_") == 0 ? T.property :
T.identifier), Integer.MAX_VALUE, ident).setName(myName);
+ theToken = SV.newSV(
+ (identLC.indexOf("property_") == 0 ? T.property : T.identifier),
+ Integer.MAX_VALUE, ident).setName(myName);
}
return theTok = theToken.tok;
}
Modified: trunk/Jmol/src/org/jmol/script/T.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/T.java 2016-02-18 04:47:00 UTC (rev
20964)
+++ trunk/Jmol/src/org/jmol/script/T.java 2016-02-27 18:59:52 UTC (rev
20965)
@@ -1414,8 +1414,6 @@
public static T getTokenFromName(String name) {
// this one needs to NOT be lower case for ScriptCompiler
- if (name == null)
- System.out.println("???");
return tokenMap.get(name);
}
Modified: trunk/Jmol/src/org/jmol/shapespecial/Polyhedra.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapespecial/Polyhedra.java 2016-02-18 04:47:00 UTC
(rev 20964)
+++ trunk/Jmol/src/org/jmol/shapespecial/Polyhedra.java 2016-02-27 18:59:52 UTC
(rev 20965)
@@ -355,8 +355,9 @@
for (int i = polyhedronCount; --i >= 0;) {
Polyhedron p = polyhedrons[i];
p.info = null;
- int mi = (p.id == null ? p.centralAtom.mi : p.modelIndex);
- if (mi == modelIndex) {
+ if (p.modelIndex > modelIndex) {
+ p.modelIndex--;
+ } else if (p.modelIndex == modelIndex) {
polyhedronCount--;
polyhedrons = (Polyhedron[]) AU.deleteElements(polyhedrons, i, 1);
}
@@ -453,7 +454,7 @@
if (property == "allInfo") {
Lst<Map<String, Object>> info = new Lst<Map<String, Object>>();
for (int i = polyhedronCount; --i >= 0;)
- info.addLast(polyhedrons[i].getInfo(vwr, true));
+ info.addLast(polyhedrons[i].getInfo(vwr, false));
data[1] = info;
return true;
}
@@ -461,7 +462,7 @@
p = findPoly(id, iatom, true);
if (p == null)
return false;
- data[1] = p.getInfo(vwr, true);
+ data[1] = p.getInfo(vwr, false);
return true;
}
return getPropShape(property, data);
@@ -504,7 +505,7 @@
public Lst<Map<String, Object>> getShapeDetail() {
Lst<Map<String, Object>> lst = new Lst<Map<String, Object>>();
for (int i = 0; i < polyhedronCount; i++)
- lst.addLast(polyhedrons[i].getInfo(vwr, true));
+ lst.addLast(polyhedrons[i].getInfo(vwr, false));
return lst;
}
@@ -526,7 +527,7 @@
for (int i = 0; i < polyhedronCount; ++i) {
Polyhedron p = polyhedrons[i];
if (bs.get(i)) {
- if (p.id == null)
+ if (colixes != null && p.id == null)
setColixAndPalette(C.INHERIT_ALL, pid, p.centralAtom.i);
continue;
}
@@ -1078,7 +1079,7 @@
if (p.id == null) {
if (ms.at[p.centralAtom.i].isDeleted())
p.isValid = false;
- p.visibilityFlags = (p.visible && bsModels.get(p.centralAtom.mi)
+ p.visibilityFlags = (p.visible && bsModels.get(p.modelIndex)
&& !ms.isAtomHidden(p.centralAtom.i)
&& !ms.at[p.centralAtom.i].isDeleted() ? vf : 0);
if (p.visibilityFlags != 0)
Modified: trunk/Jmol/src/org/jmol/shapespecial/Polyhedron.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapespecial/Polyhedron.java 2016-02-18
04:47:00 UTC (rev 20964)
+++ trunk/Jmol/src/org/jmol/shapespecial/Polyhedron.java 2016-02-27
18:59:52 UTC (rev 20965)
@@ -77,10 +77,14 @@
int[][] triangles, int triangleCount, int[][] faces, V3[] normals, BS
bsFlat, boolean collapsed, float distanceRef) {
this.distanceRef = distanceRef;
- centralAtom = (id == null ? (Atom) atomOrPt : null);
- center = (centralAtom == null ? (P3) atomOrPt : null);
- this.modelIndex = (centralAtom == null ? modelIndex : centralAtom.mi);
- this.id = id;
+ if (id == null) {
+ centralAtom = (Atom) atomOrPt;
+ this.modelIndex = centralAtom.mi;
+ } else {
+ this.id = id;
+ center = atomOrPt;
+ this.modelIndex = modelIndex;
+ }
this.nVertices = vertexCount;
this.vertices = new P3[nPoints + 1];
this.normals = new V3[triangleCount];
@@ -177,12 +181,43 @@
return ai;
}
- Map<String, Object> getInfo(Viewer vwr, boolean isAll) {
- if (isAll && this.info != null && !Logger.debugging)
+ Map<String, Object> getInfo(Viewer vwr, boolean isState) {
+ if (!isState && this.info != null && !Logger.debugging)
return this.info;
Map<String, Object> info = new Hashtable<String, Object>();
- int mi = (id == null ? centralAtom.mi : modelIndex);
- if (isAll) {
+
+ info.put("vertexCount", Integer.valueOf(nVertices));
+
+ // get COPY of vertices to prevent script variable from referencing Atom
+ int nv = (isState ? vertices.length : nVertices);
+ P3[] pts = new P3[nv];
+ for (int i = 0; i < nv; i++)
+ pts[i] = P3.newP(vertices[i]);
+ info.put("vertices", pts);
+
+ int[] elemNos = new int[nVertices];
+ for (int i = 0; i < nVertices; i++) {
+ P3 pt = vertices[i];
+ elemNos[i] = (pt instanceof Node ? ((Node) pt).getElementNumber()
+ : pt instanceof Point3fi ? ((Point3fi) pt).sD : -2);
+ }
+ info.put("elemNos", elemNos);
+
+ if (id == null) {
+ info.put("atomIndex", Integer.valueOf(centralAtom.i));
+ } else {
+ info.put("id", id);
+ info.put("center", P3.newP(center));
+ info.put("color", C.getHexCode(colix));
+ info.put("colorEdge", C.getHexCode(colixEdge == 0 ? colix : colixEdge));
+ if (offset != null)
+ info.put("offset", offset);
+ if (scale != 1)
+ info.put("scale", Float.valueOf(scale));
+ }
+ if (id != null || !isState)
+ info.put("modelIndex", Integer.valueOf(modelIndex));
+ if (!isState) {
this.info = info;
if (id == null) {
info.put("center", P3.newP(centralAtom));
@@ -196,40 +231,38 @@
}
info.put("triangleCount", Integer.valueOf(triangles.length));
info.put("volume", getVolume());
+
String[] names = new String[nVertices];
+ int[] indices = new int[nVertices];
for (int i = nVertices; --i >= 0;) {
P3 pt = vertices[i];
- names[i] = (pt instanceof Node ? ((Node) pt).getAtomName()
+ boolean isNode = pt instanceof Node;
+ names[i] = (isNode ? ((Node) pt).getAtomName()
: pt instanceof Point3fi ? Elements
.elementSymbolFromNumber(((Point3fi) pt).sD) : "");
+ indices[i] = (isNode ? ((Node) pt).getIndex() : -1);
}
+ info.put("atomNames", names);
+ info.put("vertexIndices", indices);
+
if (faces != null)
info.put("faceCount", Integer.valueOf(faces.length));
- info.put("atomNames", names);
+
if (smarts != null)
info.put("smarts", smarts);
if (smiles != null)
info.put("smiles", smiles);
if (polySmiles != null)
info.put("polySmiles", polySmiles);
+
if (pointGroup != null)
info.put("pointGroup", pointGroup.getPointGroupName());
if (pointGroupFamily != null)
info.put("pointGroupFamily", pointGroupFamily.getPointGroupName());
}
- if (id != null) {
- info.put("id", id);
- info.put("modelIndex", Integer.valueOf(mi));
- info.put("color", C.getHexCode(colix));
- info.put("colorEdge", C.getHexCode(colixEdge == 0 ? colix : colixEdge));
- if (offset != null)
- info.put("offset", offset);
- if (scale != 1)
- info.put("scale", Float.valueOf(scale));
- }
if (faces != null)
info.put("faces", faces);
- if (!isAll || Logger.debugging) {
+ if (isState || Logger.debugging) {
info.put("bsFlat", bsFlat);
if (collapsed)
info.put("collapsed", Boolean.valueOf(collapsed));
@@ -241,22 +274,6 @@
info.put("normals", n);
info.put("triangles", AU.arrayCopyII(triangles, triangles.length));
}
- info.put("vertexCount", Integer.valueOf(nVertices));
- if (center == null) {
- info.put("atomIndex", Integer.valueOf(centralAtom.i));
- } else {
- info.put("id", id);
- info.put("center", P3.newP(center));
- }
- info.put("vertices",
- AU.arrayCopyPt(vertices, (isAll ? nVertices : vertices.length)));
- int[] elemNos = new int[nVertices];
- for (int i = 0; i < nVertices; i++) {
- P3 pt = vertices[i];
- elemNos[i] = (pt instanceof Node ? ((Node) pt).getElementNumber()
- : pt instanceof Point3fi ? ((Point3fi) pt).sD : -2);
- }
- info.put("elemNos", elemNos);
return info;
}
@@ -330,7 +347,7 @@
String getState(Viewer vwr) {
String ident = (id == null ? "({"+centralAtom.i+"})" : "ID " +
Escape.e(id));
- return " polyhedron" + " @{" + Escape.e(getInfo(vwr, false)) + "} "
+ return " polyhedron" + " @{" + Escape.e(getInfo(vwr, true)) + "} "
+ (isFullyLit ? " fullyLit" : "") + ";"
+ (visible ? "" : "polyhedra " + ident + " off;") + "\n";
}
Modified: trunk/Jmol/src/org/jmol/util/MeshSlicer.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/MeshSlicer.java 2016-02-18 04:47:00 UTC
(rev 20964)
+++ trunk/Jmol/src/org/jmol/util/MeshSlicer.java 2016-02-27 18:59:52 UTC
(rev 20965)
@@ -241,7 +241,7 @@
wPlane = 0;
}
}
-
+
if (fData == null) {
if (tokType == T.decimal && bsSource != null) {
if (m.vertexSource == null)
@@ -257,8 +257,7 @@
if (m.pc == 0) {
for (int i = m.mergeVertexCount0; i < m.vc; i++) {
if (Float.isNaN(fData[i])
- || checkSlab(tokType, m.vs[i], fData[i], distance,
- bsSource) > 0)
+ || checkSlab(tokType, m.vs[i], fData[i], distance, bsSource) > 0)
m.bsSlabDisplay.clear(i);
}
return;
@@ -266,40 +265,58 @@
if (ptCenters != null || isGhost)
andCap = false; // can only cap faces, and no capping of ghosts
if (andCap && capper == null)
- capper = ((MeshCapper)
Interface.getInterface("org.jmol.util.MeshCapper", m.vwr, "script")).set(this);
+ capper = ((MeshCapper) Interface.getInterface("org.jmol.util.MeshCapper",
+ m.vwr, "script")).set(this);
if (capper != null)
capper.clear();
double absD = Math.abs(distance);
Map<String, Integer> mapEdge = new Hashtable<String, Integer>();
+ BS bsD = BS.newN(m.vc);
+ float[] d = new float[m.vc];
+ float d1 = 0, d2 = 0, d3 = 0, valA, valB, valC;
for (int i = m.mergePolygonCount0, iLast = m.pc; i < iLast; i++) {
- float d1, d2, d3, valA, valB, valC;
- int[] face = m.setABC(i);
+ int[] face = m.setABC(i);
if (face == null)
continue;
BS bsSlab = (m.bsSlabGhost != null && m.bsSlabGhost.get(i) ?
m.bsSlabGhost
: m.bsSlabDisplay);
int check1 = face[MeshSurface.P_CHECK];
int iContour = (m.dataOnly ? 0 : face[MeshSurface.P_CONTOUR]);
- T3 vA = m.vs[m.iA];
- T3 vB = m.vs[m.iB];
- T3 vC = m.vs[m.iC];
- valA = fData[m.iA];
- valB = fData[m.iB];
- valC = fData[m.iC];
+ int ia = m.iA;
+ int ib = m.iB;
+ int ic = m.iC;
+ T3 vA = m.vs[ia];
+ T3 vB = m.vs[ib];
+ T3 vC = m.vs[ic];
+ valA = fData[ia];
+ valB = fData[ib];
+ valC = fData[ic];
if (m.vertexSource != null) {
- sources[0] = m.vertexSource[m.iA];
- sources[1] = m.vertexSource[m.iB];
- sources[2] = m.vertexSource[m.iC];
+ sources[0] = m.vertexSource[ia];
+ sources[1] = m.vertexSource[ib];
+ sources[2] = m.vertexSource[ic];
}
- int thisSet = (m.vertexSets == null ? 0 : m.vertexSets[m.iA]);
- d1 = checkSlab(tokType, vA, valA, (bsSource == null ? distance
- : sources[0]), bsSource);
- d2 = checkSlab(tokType, vB, valB, (bsSource == null ? distance
- : sources[1]), bsSource);
- d3 = checkSlab(tokType, vC, valC, (bsSource == null ? distance
- : sources[2]), bsSource);
+ if (!bsD.get(ia)) {
+ bsD.set(ia);
+ d[ia] = checkSlab(tokType, vA, valA, (bsSource == null ? distance
+ : sources[0]), bsSource);
+ }
+ if (!bsD.get(ib)) {
+ bsD.set(ib);
+ d[ib] = checkSlab(tokType, vB, valB, (bsSource == null ? distance
+ : sources[1]), bsSource);
+ }
+ if (!bsD.get(ic)) {
+ bsD.set(ic);
+ d[ic] = checkSlab(tokType, vC, valC, (bsSource == null ? distance
+ : sources[2]), bsSource);
+ }
+ d1 = d[ia];
+ d2 = d[ib];
+ d3 = d[ic];
int test1 = (d1 != 0 && d1 < 0 ? 1 : 0) + (d2 != 0 && d2 < 0 ? 2 : 0)
+ (d3 != 0 && d3 < 0 ? 4 : 0);
+ int thisSet = (m.vertexSets == null ? 0 : m.vertexSets[ia]);
/*
if (iA == 955 || iB == 955 || iC == 955) {
@@ -340,8 +357,7 @@
case 6:
// BC on same side
if (ptCenters == null)
- p = new P3[] {
- interpolatePoint(vA, vB, -d1, d2, valA, valB, 0),
+ p = new P3[] { interpolatePoint(vA, vB, -d1, d2, valA, valB, 0),
interpolatePoint(vA, vC, -d1, d3, valA, valC, 1) };
else
p = new P3[] {
@@ -352,8 +368,7 @@
case 5:
//AC on same side
if (ptCenters == null)
- p = new P3[] {
- interpolatePoint(vB, vA, -d2, d1, valB, valA, 1),
+ p = new P3[] { interpolatePoint(vB, vA, -d2, d1, valB, valA, 1),
interpolatePoint(vB, vC, -d2, d3, valB, valC, 0) };
else
p = new P3[] {
@@ -364,8 +379,7 @@
case 4:
//AB on same side need A-C, B-C
if (ptCenters == null)
- p = new P3[] {
- interpolatePoint(vC, vA, -d3, d1, valC, valA, 0),
+ p = new P3[] { interpolatePoint(vC, vA, -d3, d1, valC, valA, 0),
interpolatePoint(vC, vB, -d3, d2, valC, valB, 1) };
else
p = new P3[] {
@@ -405,32 +419,32 @@
boolean tossBC = (test1 == 1);
if (tossBC || isGhost) {
// 1: BC on side to toss -- +tossBC+isGhost -tossBC+isGhost
- if (!getDE(fracs, 0, m.iA, m.iB, m.iC, tossBC))
+ if (!getDE(fracs, 0, ia, ib, ic, tossBC))
break;
if (iD < 0)
- iD = addIntersectionVertex(p[0], values[0], sources[0],
- thisSet, mapEdge, m.iA, m.iB);
+ iD = addIntersectionVertex(p[0], values[0], sources[0], thisSet,
+ mapEdge, ia, ib);
if (iE < 0)
- iE = addIntersectionVertex(p[1], values[1], sources[0],
- thisSet, mapEdge, m.iA, m.iC);
+ iE = addIntersectionVertex(p[1], values[1], sources[0], thisSet,
+ mapEdge, ia, ic);
bs = (tossBC ? bsSlab : m.bsSlabGhost);
- m.addPolygonV3(m.iA, iD, iE, check1 & 5 | 2, iContour, 0, bs);
+ m.addPolygonV3(ia, iD, iE, check1 & 5 | 2, iContour, 0, bs);
if (!isGhost)
break;
}
// BC on side to keep -- -tossBC+isGhost, +tossBC+isGhost
- if (!getDE(fracs, 1, m.iA, m.iC, m.iB, tossBC))
+ if (!getDE(fracs, 1, ia, ic, ib, tossBC))
break;
bs = (tossBC ? m.bsSlabGhost : bsSlab);
if (iE < 0) {
iE = addIntersectionVertex(p[0], values[0], sources[1], thisSet,
- mapEdge, m.iA, m.iB);
- m.addPolygonV3(iE, m.iB, m.iC, check1 & 3, iContour, 0, bs);
+ mapEdge, ia, ib);
+ m.addPolygonV3(iE, ib, ic, check1 & 3, iContour, 0, bs);
}
if (iD < 0) {
iD = addIntersectionVertex(p[1], values[1], sources[2], thisSet,
- mapEdge, m.iA, m.iC);
- m.addPolygonV3(iD, iE, m.iC, check1 & 4 | 1, iContour, 0, bs);
+ mapEdge, ia, ic);
+ m.addPolygonV3(iD, iE, ic, check1 & 4 | 1, iContour, 0, bs);
}
break;
case 5:
@@ -444,32 +458,32 @@
boolean tossAC = (test1 == 2);
if (tossAC || isGhost) {
//AC on side to toss
- if (!getDE(fracs, 0, m.iB, m.iC, m.iA, tossAC))
+ if (!getDE(fracs, 0, ib, ic, ia, tossAC))
break;
bs = (tossAC ? bsSlab : m.bsSlabGhost);
if (iE < 0)
- iE = addIntersectionVertex(p[0], values[0], sources[1],
- thisSet, mapEdge, m.iB, m.iA);
+ iE = addIntersectionVertex(p[0], values[0], sources[1], thisSet,
+ mapEdge, ib, ia);
if (iD < 0)
- iD = addIntersectionVertex(p[1], values[1], sources[1],
- thisSet, mapEdge, m.iB, m.iC);
- m.addPolygonV3(iE, m.iB, iD, check1 & 3 | 4, iContour, 0, bs);
+ iD = addIntersectionVertex(p[1], values[1], sources[1], thisSet,
+ mapEdge, ib, ic);
+ m.addPolygonV3(iE, ib, iD, check1 & 3 | 4, iContour, 0, bs);
if (!isGhost)
break;
}
// AC on side to keep
- if (!getDE(fracs, 1, m.iB, m.iA, m.iC, tossAC))
+ if (!getDE(fracs, 1, ib, ia, ic, tossAC))
break;
bs = (tossAC ? m.bsSlabGhost : bsSlab);
if (iD < 0) {
iD = addIntersectionVertex(p[0], values[0], sources[0], thisSet,
- mapEdge, m.iB, m.iA);
- m.addPolygonV3(m.iA, iD, m.iC, check1 & 5, iContour, 0, bs);
+ mapEdge, ib, ia);
+ m.addPolygonV3(ia, iD, ic, check1 & 5, iContour, 0, bs);
}
if (iE < 0) {
iE = addIntersectionVertex(p[1], values[1], sources[2], thisSet,
- mapEdge, m.iB, m.iC);
- m.addPolygonV3(iD, iE, m.iC, check1 & 2 | 1, iContour, 0, bs);
+ mapEdge, ib, ic);
+ m.addPolygonV3(iD, iE, ic, check1 & 2 | 1, iContour, 0, bs);
}
break;
case 4:
@@ -482,32 +496,32 @@
//
boolean tossAB = (test1 == 4);
if (tossAB || isGhost) {
- if (!getDE(fracs, 0, m.iC, m.iA, m.iB, tossAB))
+ if (!getDE(fracs, 0, ic, ia, ib, tossAB))
break;
if (iD < 0)
- iD = addIntersectionVertex(p[0], values[0], sources[2],
- thisSet, mapEdge, m.iA, m.iC); //CA
+ iD = addIntersectionVertex(p[0], values[0], sources[2], thisSet,
+ mapEdge, ia, ic); //CA
if (iE < 0)
- iE = addIntersectionVertex(p[1], values[1], sources[2],
- thisSet, mapEdge, m.iB, m.iC); //CB
+ iE = addIntersectionVertex(p[1], values[1], sources[2], thisSet,
+ mapEdge, ib, ic); //CB
bs = (tossAB ? bsSlab : m.bsSlabGhost);
- m.addPolygonV3(iD, iE, m.iC, check1 & 6 | 1, iContour, 0, bs);
+ m.addPolygonV3(iD, iE, ic, check1 & 6 | 1, iContour, 0, bs);
if (!isGhost)
break;
}
//AB on side to keep
- if (!getDE(fracs, 1, m.iC, m.iB, m.iA, tossAB))
+ if (!getDE(fracs, 1, ic, ib, ia, tossAB))
break;
bs = (tossAB ? m.bsSlabGhost : bsSlab);
if (iE < 0) {
iE = addIntersectionVertex(p[0], values[0], sources[0], thisSet,
- mapEdge, m.iA, m.iC); //CA
- m.addPolygonV3(m.iA, m.iB, iE, check1 & 5, iContour, 0, bs);
+ mapEdge, ia, ic); //CA
+ m.addPolygonV3(ia, ib, iE, check1 & 5, iContour, 0, bs);
}
if (iD < 0) {
iD = addIntersectionVertex(p[1], values[1], sources[1], thisSet,
- mapEdge, m.iB, m.iC); //CB
- m.addPolygonV3(iE, m.iB, iD, check1 & 2 | 4, iContour, 0, bs);
+ mapEdge, ib, ic); //CB
+ m.addPolygonV3(iE, ib, iD, check1 & 2 | 4, iContour, 0, bs);
}
break;
}
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2016-02-18 04:47:00 UTC
(rev 20964)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2016-02-27 18:59:52 UTC
(rev 20965)
@@ -65,8 +65,15 @@
TODO: isosurface molecular has an issue with 2gb1
TODO: slab SET will not be rendered correctly when exported because
tm.transformPoint
-Jmol.___JmolVersion="14.5.3_2016.02.17"
+Jmol.___JmolVersion="14.5.3_2016.02.27"
+bug fix: [function:"yyy",Function:"zzz"] fails to retain key capitalization
after first entry for special names
+bug fix: (JavaScript only) polyhedra not saved in state
+bug fix: (Applet) broken image in coverImage
+bug fix: polyhedra DELETE can crash Jmol if polyhedra are not colored
+
+JmolVersion="14.5.3_2016.02.17"
+
bug fix: slab/depth SET do not behave properly
bug fix: select VISIBLE is not properly set based on slab/depth SET
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